createGenomeAnnotation: Create a genome annotation object for ArchR
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

createGenomeAnnotation

R Documentation

Create a genome annotation object for ArchR

This function will create a genome annotation object that can be used for creating ArrowFiles or an ArchRProject, etc.

createGenomeAnnotation(
  genome = NULL,
  chromSizes = NULL,
  blacklist = NULL,
  filter = TRUE,
  filterChr = c("chrM")
)

`genome`	Either (i) a string that is a valid `BSgenome` or (ii) a `BSgenome` object (ie "hg38" or "BSgenome.Hsapiens.UCSC.hg38").
`chromSizes`	A `GRanges` object containing chromosome start and end coordinates.
`blacklist`	A `GRanges` object containing regions that should be excluded from analyses due to unwanted biases.
`filter`	A boolean value indicating whether non-standard chromosome scaffolds should be excluded. These "non-standard" chromosomes are defined by `filterChrGR()` and by manual annotation using the `filterChr` parameter.
`filterChr`	A character vector indicating the seqlevels that should be removed if manual removal is desired for certain seqlevels. If no manual removal is desired, `filterChr` should be set to `NULL`. If `filter` is set to `TRUE` but `filterChr` is set to `NULL`, non-standard chromosomes will still be removed as defined in `filterChrGR()`.